It's common to have packages that generate header files out of
    configure options.  If prefix changes from configure to build time,
    the header files end up incorrect.

That would be a bug, according to the present spec.

    Ok, so the right thing to do is to generate the header files at build
    time, based on `make' options, right?

Yes.

      But then, what if someone
    starts a build with `prefix=/foo', modifies some files, then re-starts
    with `prefix=/bar'?

Indeed, that would lead to bad results.

I see the point you're making.  If prefix were only a configure-time option,
that problem could not happen.  That would be an advantage.

That raises two questions:

* Is the advantage big enough to justify the incompatible change
of saying "You can't specify the prefix when you run Make"?

* What about other related Make variables, such as *dir?
Should they all be configure time options too?
If yes, that is a much bigger incompatible change.
If not, then prefix would be treated differently from the rest;
that lack of consistency is also not a good thing.

All in all, I don't see that the change is clearly an improvement.
However, it *might* be a good idea to say that all configure scripts
should accept --... args to specify all these directories and
encourage people to use them that way.  (It looks like
Autoconf-generated scripts already support them.)

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